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scRNAseq (development version)

scRNAseq

This is the development version of scRNAseq; for the stable release version, see scRNAseq.

Collection of Public Single-Cell RNA-Seq Datasets

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DOI: 10.18129/B9.bioc.scRNAseq

Bioconductor version: Development (3.23)

Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata.

Author: Davide Risso [aut, cph], Michael Cole [aut], Aaron Lun [ctb, cre], Alan O'Callaghan [ctb], Jens Preussner [ctb], Charlotte Soneson [ctb], Stephany Orjuela [ctb], Daniel Bunis [ctb], Milan Malfait [ctb]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Citation (from within R, enter citation("scRNAseq")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("scRNAseq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scRNAseq")

User's Guide HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SequencingData, SingleCellData

Version 2.25.0

License CC0

Depends SingleCellExperiment

Imports utils, methods, Matrix, BiocGenerics, S4Vectors, SparseArray, DelayedArray, GenomicRanges, SummarizedExperiment, ExperimentHub(>= 2.3.4), AnnotationHub(>= 3.3.6), AnnotationDbi, ensembldb, GenomicFeatures, alabaster.base, alabaster.matrix, alabaster.sce, gypsum, jsonlite, DBI, RSQLite

System Requirements

URL

See More

Suggests BiocStyle, knitr, rmarkdown, testthat, jsonvalidate, BiocManager

Linking To

Enhances

Depends On Me OSCA.basic, OSCA.intro, OSCA.workflows, SingleRBook

Imports Me singleCellTK

Suggests Me APL, BASiCS, batchelor, bluster, ccImpute, ClusterFoldSimilarity, Coralysis, CSOA, destiny, dittoSeq, Glimma, iSEE, iSEEfier, iSEEhex, iSEEindex, iSEEu, looking4clusters, miloR, miQC, mumosa, ReactomeGSA, scAnnotatR, scater, scDblFinder, scDiagnostics, scDotPlot, scFeatureFilter, scone, scran, scrapper, scTreeViz, scuttle, SingleCellExperiment, SingleR, SplineDV, UCell, velociraptor, zellkonverter, zinbwave, scStability, speakeasyR

Links To Me

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scRNAseq_2.25.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/scRNAseq

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scRNAseq

Package Short Url https://bioconductor.org/packages/scRNAseq/

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